rs11088086

Variant names:

• chr21-28736843-C-A
• rs11088086
• XR_007067787.1:n.936+85062G>T

Your query was ambiguous. Multiple possible variants found:

• chr21-28736843-C-A
• chr21-28736843-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007067787.1(N6AMT1):​n.936+85062G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 150,960 control chromosomes in the GnomAD database, including 6,081 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6081 hom., cov: 31)
• Consequence: N6AMT1 XR_007067787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

N6AMT1 (HGNC:16021): (N-6 adenine-specific DNA methyltransferase 1) This gene encodes an N(6)-adenine-specific DNA methyltransferase. The encoded enzyme may be involved in the methylation of release factor I during translation termination. This enzyme is also involved in converting the arsenic metabolite monomethylarsonous acid to the less toxic dimethylarsonic acid. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 11. [provided by RefSeq, Mar 2023]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
N6AMT1	XR_007067787.1	n.936+85062G>T		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41392 AN: 150882 Hom.: 6068 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.300

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.275 AC: 41450 AN: 150960 Hom.: 6081 Cov.: 31 AF XY: 0.271 AC XY: 19962 AN XY: 73662

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.301

Alfa AF: 0.133 Hom.: 269

Bravo AF: 0.295

Asia WGS AF: 0.324 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11088086; hg19: chr21-30109165;